IMP::example::ExamplePairScore Class Reference

Apply a harmonic to the distance between two particles. More...

#include <IMP/example/ExamplePairScore.h>

Inheritance diagram for IMP::example::ExamplePairScore:

Public Member Functions
	ExamplePairScore (double x0, double k)
virtual kernel::ModelObjectsTemp	do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const
double	evaluate_if_good_indexes (kernel::Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual double	evaluate_index (kernel::Model *m, const kernel::ParticleIndexPair &p, DerivativeAccumulator *da) const
	Compute the score and the derivative if needed.
double	evaluate_indexes (kernel::Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const
virtual std::string	get_type_name () const
virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object.
Public Member Functions inherited from IMP::kernel::PairScore
	PairScore (std::string name="PairScore %1%")
Restraints	create_current_decomposition (kernel::Model *m, const ParticleIndexPair &vt) const
virtual double	evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const
	Compute the score and the derivative if needed. More...
virtual double	evaluate_if_good_index (kernel::Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da, double max) const
	Compute the score and the derivative if needed.
Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp	get_input_containers (Particle *p) const
virtual ParticlesTemp	get_input_particles (Particle *p) const
ModelObjectsTemp	get_inputs (kernel::Model *m, const ParticleIndexes &pis) const
Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()
virtual void	do_destroy ()
CheckLevel	get_check_level () const
LogLevel	get_log_level () const
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...
void	set_was_used (bool tf) const
void	show (std::ostream &out=std::cout) const
const std::string &	get_name () const
void	set_name (std::string name)

Additional Inherited Members
Public Types inherited from IMP::kernel::PairScore
typedef ParticlePair	Argument
typedef ParticleIndexPair	IndexArgument
typedef PairModifier	Modifier
typedef const ParticlePair &	PassArgument
typedef const ParticleIndexPair &	PassIndexArgument
Protected Member Functions inherited from IMP::kernel::PairScore
virtual Restraints	do_create_current_decomposition (kernel::Model *m, const ParticleIndexPair &vt) const
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...
	Object ()

Detailed Description

The source code is as follows:

/**
 *  \file IMP/example/ExamplePairScore.h
 *  \brief A Score on the distance between a pair of particles.
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 */

#ifndef IMPEXAMPLE_EXAMPLE_PAIR_SCORE_H
#define IMPEXAMPLE_EXAMPLE_PAIR_SCORE_H

#include <IMP/example/example_config.h>
#include <IMP/core/XYZ.h>
#include <IMP/PairScore.h>
#include <IMP/pair_macros.h>
#include <IMP/UnaryFunction.h>
#include <IMP/base/Pointer.h>

IMPEXAMPLE_BEGIN_NAMESPACE

//! Apply a harmonic to the distance between two particles.
/** The source code is as follows:
    \include ExamplePairScore.h
    \include ExamplePairScore.cpp
*/
class IMPEXAMPLEEXPORT ExamplePairScore : public PairScore {
  double x0_, k_;

 public:
  ExamplePairScore(double x0, double k);
  virtual double evaluate_index(kernel::Model *m,
                                const kernel::ParticleIndexPair &p,
                                DerivativeAccumulator *da) const IMP_OVERRIDE;
  virtual kernel::ModelObjectsTemp do_get_inputs(kernel::Model *m, const kernel::ParticleIndexes &pis)
      const IMP_OVERRIDE;
  IMP_PAIR_SCORE_METHODS(ExamplePairScore);
  IMP_OBJECT_METHODS(ExamplePairScore);;
};

IMP_OBJECTS(ExamplePairScore, ExamplePairScores);

IMPEXAMPLE_END_NAMESPACE

#endif /* IMPEXAMPLE_EXAMPLE_PAIR_SCORE_H */

/**
 *  \file ExamplePairScore.cpp
 *  \brief A Score on the distance between a pair of particles.
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 */

#include <IMP/example/ExamplePairScore.h>
#include <IMP/core/XYZ.h>
#include <IMP/UnaryFunction.h>

#include <boost/lambda/lambda.hpp>

IMPEXAMPLE_BEGIN_NAMESPACE

ExamplePairScore::ExamplePairScore(double x0, double k) : x0_(x0), k_(k) {}

Float ExamplePairScore::evaluate_index(kernel::Model *m,
                                       const kernel::ParticleIndexPair &pip,
                                       DerivativeAccumulator *da) const {
  // turn on logging for this method
  IMP_OBJECT_LOG;
  // assume they have coordinates
  core::XYZ d0(m, pip[0]);
  core::XYZ d1(m, pip[1]);
  // log something
  double diff =
      (d0.get_coordinates() - d1.get_coordinates()).get_magnitude() - x0_;
  IMP_LOG_VERBOSE("The distance off from x0 is " << diff << std::endl);
  double score = .5 * k_ * square(diff);
  if (da) {
    // derivatives are requested
    algebra::Vector3D delta = d0.get_coordinates() - d1.get_coordinates();
    algebra::Vector3D udelta = delta.get_unit_vector();
    double dv = k_ * diff;
    // add to the particle derivatives
    d0.add_to_derivatives(udelta * dv, *da);
    d1.add_to_derivatives(-udelta * dv, *da);
  }
  return score;
}

ModelObjectsTemp ExamplePairScore::do_get_inputs(kernel::Model *m,
                                               const kernel::ParticleIndexes &pis)
    const {
  return IMP::kernel::get_particles(m, pis);
}

IMPEXAMPLE_END_NAMESPACE

Definition at line 25 of file ExamplePairScore.h.

Member Function Documentation

virtual kernel::ModelObjectsTemp IMP::example::ExamplePairScore::do_get_inputs ( kernel::Model *  m, const kernel::ParticleIndexes &  pis  ) const

virtual

Overload this method to specify the inputs.

Reimplemented from IMP::kernel::ParticleInputs.

double IMP::example::ExamplePairScore::evaluate_if_good_indexes ( kernel::Model *  m, const ParticleIndexPairs &  o, DerivativeAccumulator *  da, double  max, unsigned int  lower_bound, unsigned int  upper_bound  ) const

virtual

Implementations for these are provided by the IMP_PAIR_SCORE() macro.

Reimplemented from IMP::kernel::PairScore.

Definition at line 35 of file ExamplePairScore.h.

double IMP::example::ExamplePairScore::evaluate_indexes ( kernel::Model *  m, const ParticleIndexPairs &  o, DerivativeAccumulator *  da, unsigned int  lower_bound, unsigned int  upper_bound  ) const

virtual

Implementations for these are provided by the IMP_PAIR_SCORE() macro.

Reimplemented from IMP::kernel::PairScore.

Definition at line 35 of file ExamplePairScore.h.

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The documentation for this class was generated from the following file:

• ExamplePairScore.h